epigenetics

Epigenetics：epigenetic modifications、Epigenetic proteins、Molecular Networks……

epigenetics

• epigenetic modifications
  • On DNA
    • Methylation
      • substrate
        • cytosine
          • 5-methylcytosine
        • uracil
          • thymine
      • effects
        • no effects on base pairing, but affect major groove protein recognation
      • writing
        • only on an already turned-off gene
      • reading
        • read by proteins that block transcription activators
      • function
        • ensure a turned-off gene stay off
  • On histones
    • Methylation
      • substrate
        • core histones
      • effects
        • inactivation?
      • writing
        • generally in inactive regions of chromatin
    • Acetylation
      • substrate
        • amino tails of core histones
      • writing
        • generally in active regions of chromatin
      • erasing
        • histone deacetylase
      • effects
        • change chromatin structure, increase DNA accessiblity
• Epigenetic proteins
  • chromatin-remodeling complexes
    • components
      • enzymes
        • modify chromosomes
      • DNA
        • Change chromatin structures
    • Classes
      • ATP-dependent chromatin remodeling factors
        • catalyzes 4 processes with ATP
          • Nucleosome sliding
          • Nucleosome remodeling
            • increase DNA accessibliity
          • Nucleosome displacement
            • remove core histones
          • Histone replacement
    • function
      • heterochromatin formation
        • regulated by endogenous siR interference
  • specific transcription factors
    • some coactivators are histone acetylase
    • some corepressors are histone deacetylase
• chromatin structure organization
  • nucleosomes
    • component
      • DNA
      • histones
    • function
      • block binding of some transcription initiation factors and RNA pol II
        • i.e. reduces DNA accessibility
  • higher organizations
    • depend on histone modification states
    • further reduce DNA accessibility
• Molecular Networks
  • Metabolism networks
    • nodes
      • small cellular organic molecules
    • linkages
      • chemical reactions with enzymes catalyzing it
  • Signaling networks
    • nodes
      • receptors, signaling proteins, and secondary messengers
    • linkages
      • relay of signals
        • can be a reaction: phosphorylation
        • can be non-convalent interactions
  • Gene regulation networks
    • nodes
      • genes and regulatory proteins
    • linkages
      • events that change expression levels of genes
  • Gene coexpression networks
    • nodes
      • genes
    • linkages
      • they express together
  • Protein-Protein interaction networks
    • Nodes
      • all the proteins
    • linkages
      • non-covalent interactions